Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
Biochemistry (Mosc). 2020 Nov;85(11):1443-1457. doi: 10.1134/S0006297920110127.
Virtual screening of all possible tripeptide analogues of chloramphenicol was performed using molecular docking to evaluate their affinity to bacterial ribosomes. Chloramphenicol analogues that demonstrated the lowest calculated energy of interaction with ribosomes were synthesized. Chloramphenicol amine (CAM) derivatives, which contained specific peptide fragments from the proline-rich antimicrobial peptides were produced. It was demonstrated using displacement of the fluorescent erythromycin analogue from its complex with ribosomes that the novel peptide analogues of chloramphenicol were able to bind bacterial ribosome; all the designed tripeptide analogues and one of the chloramphenicol amine derivatives containing fragment of the proline-rich antimicrobial peptides exhibited significantly greater affinity to Escherichia coli ribosome than chloramphenicol. Correlation between the calculated and experimentally evaluated levels of the ligand efficiencies was observed. In vitro protein biosynthesis inhibition assay revealed, that the RAW-CAM analogue shows activity at the level of chloramphenicol. These data were confirmed by the chemical probing assay, according to which binding pattern of this analogue in the nascent peptide exit tunnel was similar to chloramphenicol.
采用分子对接技术对氯霉素的所有可能三肽类似物进行虚拟筛选，以评估它们与细菌核糖体的亲和力。合成了与核糖体相互作用计算能量最低的氯霉素类似物。合成了含有富含脯氨酸的抗菌肽特定肽片段的氯霉素胺（CAM）衍生物。通过从核糖体与红霉素类似物的复合物中置换荧光红霉素类似物，证明了新型氯霉素肽类似物能够与细菌核糖体结合；所有设计的三肽类似物和一个含有富含脯氨酸的抗菌肽片段的氯霉素胺衍生物对大肠杆菌核糖体的亲和力均明显大于氯霉素。观察到计算配体效率水平与实验评估水平之间的相关性。体外蛋白质生物合成抑制测定显示，RAW-CAM 类似物的活性与氯霉素相当。这些数据通过化学探测测定得到了证实，根据该测定，该类似物在新生肽出口隧道中的结合模式与氯霉素相似。
